New case study: SalmoSim – a laboratory model of the salmon gut microbiome

Helping the aquaculture sector understand how feed ingredients and additives affect salmon digestion and gut health

SalmoSim is the first laboratory-based model of the Atlantic salmon gut microbiome, developed to help the aquaculture sector better understand how feed ingredients and additives affect salmon digestion and gut health.

A SAIC‑supported project led by the University of Glasgow, SalmoSim offers a controlled, ethical, and cost‑effective way to test new feed components before moving to live fish trials. Valued at £364k, the other project partners were Alltech, Mowi Scotland, and Nofima.

Farmed salmon rely on specially formulated feeds, and their gut contains a diverse community of microbes that plays an important role in nutrition, immunity, and overall wellbeing. Traditionally, researchers have tested new additives, e.g., probiotics and prebiotics, directly in live salmon. These trials are expensive, time‑consuming, and often require large numbers of fish.

Inspired by human gut simulators, the SalmoSim team built a system of bioreactors that replicate key parts of the salmon digestive tract, including temperature, acidity, oxygen levels, and microbial communities. The project involved three major steps: characterising the natural salmon microbiome, adapting bioreactors to simulate gut conditions, and comparing how SalmoSim responds to diet changes relative to real salmon. Early trials showed that the system can mirror the biological responses seen in live fish.

Alltech used SalmoSim to test a prebiotic and the system was used to measure changes in gut microbes, antimicrobial activity, and production of beneficial fatty acids. The team is also developing ways to estimate feed digestibility, offering an additional tool for feed manufacturers.

Since the project’s completion, SalmoSim has attracted interest from companies seeking to screen new feed ingredients and went on to secure commercial contracts.

The full title of this project is ‘Simulating in vitro Atlantic salmon intestinal microbiome system’.

 

 

Read the case study